Ah! Yes. I changed directories to my subjects_dir and the command worked.
I then re-tried my original mri_vol2vol script. * * *mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz * *--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz * *--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat * *--inv --o FSL_MNI305_2mm.nii.gz* * * Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview.
On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Oh I see. You probably don't have write access to the current directory (which I assume to be * /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)*, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory.
--Thomas
On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach pabeach1@gmail.com wrote:
I'm getting the same error, despite doing just that. :-/
*[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz* *mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz...
*TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
You have to give it the full path:
*mri_convert **/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz*
*--Thomas*
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabeach1@gmail.com wrote:
The mri_convert command did not work...
*[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz* *mri_convert mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from mni305.cor.mgz...* *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.comwrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks
fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
> Hi Paul, > > Just to clarify, > > 1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in > your other software? > > 2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, > does it look mis-oriented in your other software? > > --Thomas > > > On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.comwrote: > >> Hi Thomas, >> >> Thank you for the advice. >> >> I ran: >> *tkmedit FSL_MNI305_2mm.nii.gz \ >> /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz >> * >> * >> * >> and tkmedit opened the transformed subject. >> >> This is what I see: >> [image: Inline image 1] >> >> So in tkmedit it is oriented properly. However, I utilize AFNI just >> as much as Freesurfer in viewing results (my functional data is not ran >> through fsfast). So, not having things oriented properly in other viewers >> is problematic. >> >> >> On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote: >> >>> That's strange. FSL_MNI152_FreeSurferConformed_1mm.nii.gz should >>> correspond exactly to norm.mgz obtained from running >>> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz through >>> recon-all (FS4.5). >>> >>> So Doug's command should work as well. Just to confirm, can you >>> run >>> >>> >> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz >>> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>> >>> The two templates should be exactly overlapping. >>> >>> --Thomas >>> >>> >>> On Tue, Oct 1, 2013 at 9:40 PM, Paul Beach pabeach1@gmail.comwrote: >>> >>>> Doug, >>>> >>>> Unfortunately I cannot load this volume into tkmedit as this is >>>> not a subject that has been ran through Freesurfer - it's the downloadable >>>> FSL-based T1 volume from the "Yeo_JNeurophysiol11_MNI152" package available >>>> on the Freesurfer website. I'm trying to convert this and subsequent >>>> functional networks to MNI305 for connectivity analysis. >>>> >>>> However, I did open up the results in FSLview and Freeview. I >>>> have attached screen shots of each, respectively. >>>> FSLview >>>> [image: Inline image 1] >>>> Freeview >>>> [image: Inline image 2] >>>> >>>> Again, these images are resultant from the following script: >>>> *mri_vol2vol --mov >>>> /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz >>>> * >>>> *--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz * >>>> *--reg >>>> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat * >>>> *--inv --o FSL_MNI305_2mm.nii.gz* >>>> >>>> >>>> Thanks, >>>> Paul >>>> >>>> >>>> >>>> On Mon, Sep 30, 2013 at 7:46 PM, Douglas N Greve < >>>> greve@nmr.mgh.harvard.edu> wrote: >>>> >>>>> >>>>> View it in tkmedit to see if it is really a problem with your >>>>> vol2vol command. >>>>> doug >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 09/30/2013 07:33 PM, Paul Beach wrote: >>>>> >>>>>> No. That was just a general example of how the image looks - >>>>>> from a stock google image of an FSL brain (I'm not in the lab and so cannot >>>>>> put up actual images). I've been using AFNI to view them. >>>>>> >>>>>> >>>>>> On Mon, Sep 30, 2013 at 7:23 PM, Douglas N Greve < >>>>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> >>>>>> wrote: >>>>>> >>>>>> Is this in tkmedit? >>>>>> >>>>>> >>>>>> On 09/30/2013 06:59 PM, Paul Beach wrote: >>>>>> >>>>>> Hi Doug, >>>>>> >>>>>> Sorry, I should have been more specific. I meant for >>>>>> when one >>>>>> looks at the resulting transformation in a sagittal >>>>>> view. >>>>>> >>>>>> More specifically... >>>>>> Instead of this: >>>>>> Inline image 1 >>>>>> >>>>>> It looks more like this (though more like a 70degree >>>>>> shift >>>>>> than 90): >>>>>> Inline image 2 >>>>>> The other views are obviously affected as well. >>>>>> Performing a >>>>>> dataset "nudge" using afni generally "corrects" this >>>>>> problem, >>>>>> but I'd like to prevent it from happening in the first >>>>>> place. >>>>>> >>>>>> I'm suspicious that this is occurring because I'm using >>>>>> '/mni305.cor.mgz/' instead of '/mni305.2mm.nii.gz/' for >>>>>> the >>>>>> 'mov' command. However, I don't have the latter file >>>>>> anywhere >>>>>> in my Freesurfer directory. The former file is the >>>>>> closest >>>>>> thing I could find. >>>>>> >>>>>> >>>>>> Thoughts? >>>>>> Paul >>>>>> >>>>>> >>>>>> >>>>>> On Mon, Sep 30, 2013 at 5:52 PM, Douglas N Greve >>>>>> <greve@nmr.mgh.harvard.edu mailto: >>>>> greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>>> >>>>>> wrote: >>>>>> >>>>>> what do you mean the frontal lobe is pointing >>>>>> straight up? >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 09/30/2013 02:32 PM, Paul Beach wrote: >>>>>> > Freesurfer experts, >>>>>> > >>>>>> > I'm attempting to utilize an archived e-mail's >>>>>> contents >>>>>> to resample >>>>>> > data in MNI152 to 305. >>>>>> > >>>>>> > The script I'm using is as follows: >>>>>> > /mri_vol2vol / >>>>>> > /--mov >>>>>> > >>>>>> /extern/research/tools/** >>>>>> freesurfer-5.3.0/subjects/**fsaverage/mri.2mm/mni305.cor.**mgz >>>>>> > / >>>>>> > /--targ FSL_MNI152_**FreeSurferConformed_1mm.nii.gz >>>>>> / >>>>>> > /--reg >>>>>> $FREESURFER_HOME/subjects/** >>>>>> fsaverage/mri.2mm/reg.2mm.**mni152.dat / >>>>>> > /--inv --o FSL_MNI305_2mm.nii.gz/ >>>>>> > / >>>>>> > / >>>>>> > / >>>>>> > / >>>>>> > This series of commands is based on the following >>>>>> suggestion >>>>>> from Doug >>>>>> > in a previously archived e-mail exchange from >>>>>> someone >>>>>> attempting >>>>>> to do >>>>>> > something similar: >>>>>> > />> To go from mni152 to the MNI305 2mm space, >>>>>> use/ >>>>>> > />>/ >>>>>> > />> mri_vol2vol --mov mni305.2mm.nii.gz / >>>>>> > />> --targ $FSLDIR/data/standard/MNI152_**T1_2mm.nii.gz >>>>>> / >>>>>> > />> --reg >>>>>> > >>>>>> $FREESURFER_HOME/subjects/**fsaverage/mri.2mm/reg.2mm.* >>>>>> *mni152.dat / >>>>>> > />> --inv --o output.mni305.2mm.nii.gz/ >>>>>> > />>/ >>>>>> > />> This will resample MNI152_T1_2mm.nii.gz (or >>>>>> anything >>>>>> in that >>>>>> > space) to the/ >>>>>> > />> mni305 2mm space./ >>>>>> > >>>>>> > >>>>>> > However, this changing the orientation of my data >>>>>> - >>>>>> essentially all >>>>>> > images are being rotated 90degrees so the frontal >>>>>> lobe >>>>>> is pointed >>>>>> > straight up. >>>>>> > >>>>>> > Are there any suggestions to ameliorate this >>>>>> problem? >>>>>> > >>>>>> > Thanks! >>>>>> > -- >>>>>> > Paul Beach >>>>>> > DO/PhD candidate - Year VI >>>>>> > Michigan State University >>>>>> > - College of Osteopathic Medicine >>>>>> > - Neuroscience Program >>>>>> > - Bozoki Lab: Neurology/Radiology >>>>>> > >>>>>> > >>>>>> > ______________________________**_________________ >>>>>> > Freesurfer mailing list >>>>>> > Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> > >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >> >>>>>> >>>>>> > https://mail.nmr.mgh.harvard.** >>>>>> edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu mailto: >>>>> greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>>> >> >>>>>> Phone Number: 617-724-2358 tel:617-724-2358 >>>>>> <tel:617-724-2358 tel:617-724-2358> >>>>>> Fax: 617-726-7422 tel:617-726-7422 tel: >>>>> 617-726-7422 >>>>>> >>>>>> tel:617-726-7422> >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/** >>>>>> fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> > >>>>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> > >>>>>> FileDrop: https://gate.nmr.mgh.harvard.** >>>>>> edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.** >>>>> edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> > >>>>>> http://www.nmr.mgh.harvard.** >>>>> edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> > >>>>>> >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.** >>>>>> edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> ______________________________**_________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> > >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >> >>>>>> >>>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>>>>> freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for >>>>>> the >>>>>> person to >>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to >>>>>> you in >>>>>> error and >>>>>> the e-mail >>>>>> contains patient information, please contact the >>>>>> Partners >>>>>> Compliance HelpLine at >>>>>> http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to >>>>>> you in error >>>>>> but does not contain patient information, please >>>>>> contact the >>>>>> sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- Paul Beach >>>>>> DO/PhD candidate - Year VI >>>>>> Michigan State University >>>>>> - College of Osteopathic Medicine >>>>>> - Neuroscience Program >>>>>> - Bozoki Lab: Neurology/Radiology >>>>>> >>>>>> >>>>>> -- Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.** >>>>> edu greve@nmr.mgh.harvard.edu> >>>>>> Phone Number: 617-724-2358 tel:617-724-2358 >>>>>> Fax: 617-726-7422 tel:617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> > >>>>>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.* >>>>> *htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> > >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/* >>>>>> *greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Paul Beach >>>>>> DO/PhD candidate - Year VI >>>>>> Michigan State University >>>>>> - College of Osteopathic Medicine >>>>>> - Neuroscience Program >>>>>> - Bozoki Lab: Neurology/Radiology >>>>>> >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.** >>>>> edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> >>>> >>>> >>>> -- >>>> Paul Beach >>>> DO/PhD candidate - Year VI >>>> Michigan State University >>>> - College of Osteopathic Medicine >>>> - Neuroscience Program >>>> - Bozoki Lab: Neurology/Radiology >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is >>>> addressed. If you believe this e-mail was sent to you in error >>>> and the e-mail >>>> contains patient information, please contact the Partners >>>> Compliance HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent >>>> to you in error >>>> but does not contain patient information, please contact the >>>> sender and properly >>>> dispose of the e-mail. >>>> >>>> >>> >> >> >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program >> - Bozoki Lab: Neurology/Radiology >> > >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
